library(tidyverse)
library(readr)
library(dplyr)
library(ggplot2)
library(stringr)
library(cowplot)
library(RColorBrewer)
library(purrr)
library(shiny)
library(DT)
2´,3´-cyclic phosphate RNA-sequencing libraries were prepared from mouse macrophages: B6 (WT), IFNAR KO, RNaseL KO. These cells were either mock infected or infected with WT MHV virus (from Volker or Susan), MHV mutated to inactivate ns2 (phosphodiesterase) activity, or MHV mutated to inactivate nsp15 (endoribonuclease) activity for 9 and 12 hours.
sample_info_table <- read_tsv("sample_info.txt", col_names = c("cell type", "virus type", "time"))
datatable(sample_info_table)
These libraries were processed to generate bedgraph files containing sites of 3´-cleavage and the associated dinucleotide in the MHV (+) strand RNA (mRNA) and (-) strand RNA (genomic).
Coverage plots for all cell types by type of viral infection
These plots show the normalized counts of captured 2´,3´-cyclic phosphates captured (% of total cDNA reads for each library) per nucleotide position in the the MHV (+) strand reads. The MHV (-) strand reads are displayed using un-normalized counts because there were very few detected cleavage events and those occured at very low frequency.
#MHV (+) strand coverage plots
data_dir_neg = "~/Dropbox (Hesselberth Lab)/Rachel_data/EndoU_project/viral_bg/neg"
data_files_neg = list.files(data_dir_neg, full.names = T)
read_file <- function(x) {
df <- readr::read_tsv(x, col_names = c("chrom", "start", "end", "count", "normalized_count", "dinuc"))
df$name <- basename(x)
df
}
neg_table <- purrr::map_df(data_files_neg, read_file) %>%
mutate(name = str_replace(name, ".mhv.neg.dinuc.bg", "")) %>%
separate(name, into = c('cell', 'virus', 'time'), sep = '_')
datatable(neg_table)